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OnClass.data-00000-of-00001

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OnClass.npz

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accuracies.json

@@ -1,4 +1,4 @@
 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 1679 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| neutrophil | 1501 | 0.99 | 1.00 | 0.99 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta T cell | 1092 | 0.81 | 0.91 | 0.91 | 0.89 | 0.00 | 0.85 | 0.79 | 0.84 | 0.90 |\n| classical monocyte | 443 | 0.81 | 0.88 | 0.87 | 0.85 | 0.00 | 0.81 | 0.83 | 0.84 | 0.90 |\n| plasma cell | 370 | 0.99 | 0.97 | 0.99 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |\n| natural killer cell | 379 | 0.93 | 0.94 | 0.96 | 0.91 | 0.00 | 0.94 | 0.93 | 0.94 | 0.94 |\n| monocyte | 337 | 0.70 | 0.78 | 0.78 | 0.75 | 0.00 | 0.74 | 0.66 | 0.72 | 0.81 |\n| macrophage | 280 | 0.91 | 0.95 | 0.95 | 0.94 | 0.00 | 0.93 | 0.92 | 0.94 | 0.97 |\n| CD4-positive, alpha-beta T cell | 285 | 0.29 | 0.58 | 0.55 | 0.48 | 0.00 | 0.53 | 0.42 | 0.51 | 0.55 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 216 | 0.60 | 0.67 | 0.67 | 0.55 | 0.00 | 0.65 | 0.59 | 0.70 | 0.70 |\n| endothelial cell | 120 | 0.97 | 0.98 | 0.97 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| mature NK T cell | 110 | 0.66 | 0.73 | 0.75 | 0.48 | 0.00 | 0.65 | 0.60 | 0.70 | 0.75 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 61 | 0.47 | 0.17 | 0.62 | 0.19 | 0.00 | 0.50 | 0.46 | 0.54 | 0.61 |\n| erythrocyte | 45 | 0.84 | 0.99 | 0.97 | 0.98 | 0.00 | 0.98 | 0.98 | 0.93 | 0.98 |\n| intermediate monocyte | 30 | 0.10 | 0.00 | 0.14 | 0.10 | 0.00 | 0.19 | 0.20 | 0.32 | 0.39 |\n| regulatory T cell | 30 | 0.45 | 0.53 | 0.47 | 0.24 | 0.00 | 0.35 | 0.38 | 0.44 | 0.48 |\n| innate lymphoid cell | 23 | 0.79 | 0.90 | 0.94 | 0.89 | 0.00 | 0.79 | 0.92 | 0.84 | 0.90 |\n| T cell | 13 | 0.65 | 0.69 | 0.67 | 0.67 | 0.00 | 0.36 | 0.62 | 0.50 | 0.63 |\n| non-classical monocyte | 13 | 0.00 | 0.00 | 0.25 | 0.12 | 0.00 | 0.36 | 0.35 | 0.46 | 0.38 |\n| hematopoietic precursor cell | 9 | 0.33 | 0.80 | 0.67 | 0.75 | 0.00 | 0.62 | 0.70 | 0.84 | 0.94 |\n| platelet | 6 | 0.00 | 0.67 | 0.67 | 0.83 | 0.00 | 0.48 | 1.00 | 0.86 | 1.00 |\n| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.67 | 0.67 | 0.00 | 0.27 | 0.80 | 0.67 | 0.50 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| hematopoietic stem cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 14878 | 0.99 | 0.99 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| neutrophil | 13400 | 0.99 | 0.99 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta T cell | 9795 | 0.82 | 0.92 | 0.95 | 0.93 | 0.00 | 0.86 | 0.81 | 0.85 | 0.92 |\n| classical monocyte | 4019 | 0.81 | 0.85 | 0.90 | 0.88 | 0.00 | 0.83 | 0.82 | 0.85 | 0.91 |\n| plasma cell | 3606 | 0.99 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 3565 | 0.93 | 0.94 | 0.97 | 0.94 | 0.00 | 0.95 | 0.94 | 0.95 | 0.96 |\n| monocyte | 2777 | 0.67 | 0.73 | 0.83 | 0.79 | 0.00 | 0.71 | 0.71 | 0.76 | 0.83 |\n| macrophage | 2526 | 0.91 | 0.94 | 0.96 | 0.95 | 0.00 | 0.93 | 0.94 | 0.94 | 0.96 |\n| CD4-positive, alpha-beta T cell | 2457 | 0.30 | 0.54 | 0.68 | 0.64 | 0.00 | 0.56 | 0.50 | 0.60 | 0.67 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 2101 | 0.66 | 0.61 | 0.79 | 0.72 | 0.00 | 0.74 | 0.70 | 0.76 | 0.81 |\n| endothelial cell | 1230 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |\n| mature NK T cell | 919 | 0.73 | 0.78 | 0.86 | 0.66 | 0.00 | 0.73 | 0.70 | 0.75 | 0.85 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 561 | 0.47 | 0.07 | 0.76 | 0.47 | 0.00 | 0.51 | 0.54 | 0.56 | 0.66 |\n| erythrocyte | 361 | 0.84 | 0.98 | 0.98 | 0.98 | 0.00 | 0.96 | 0.99 | 0.96 | 0.98 |\n| intermediate monocyte | 366 | 0.14 | 0.02 | 0.35 | 0.31 | 0.00 | 0.37 | 0.45 | 0.49 | 0.64 |\n| regulatory T cell | 312 | 0.46 | 0.43 | 0.62 | 0.39 | 0.00 | 0.55 | 0.58 | 0.66 | 0.72 |\n| innate lymphoid cell | 147 | 0.71 | 0.80 | 0.90 | 0.84 | 0.00 | 0.75 | 0.90 | 0.89 | 0.89 |\n| T cell | 138 | 0.65 | 0.65 | 0.76 | 0.66 | 0.00 | 0.44 | 0.72 | 0.55 | 0.71 |\n| non-classical monocyte | 113 | 0.00 | 0.00 | 0.49 | 0.08 | 0.00 | 0.50 | 0.62 | 0.70 | 0.74 |\n| hematopoietic precursor cell | 59 | 0.21 | 0.70 | 0.82 | 0.78 | 0.00 | 0.65 | 0.79 | 0.85 | 0.87 |\n| platelet | 48 | 0.00 | 0.59 | 0.67 | 0.83 | 0.00 | 0.39 | 0.86 | 0.86 | 0.97 |\n| myeloid dendritic cell | 15 | 0.00 | 0.00 | 0.56 | 0.21 | 0.00 | 0.22 | 0.86 | 0.88 | 0.93 |\n| plasmacytoid dendritic cell | 6 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.31 | 1.00 | 0.86 | 1.00 |\n| basophil | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 1.00 | 1.00 | 1.00 |\n| hematopoietic stem cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 1.00 | 1.00 | 0.67 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 1681 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| neutrophil | 1515 | 0.99 | 1.00 | 1.00 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta T cell | 1070 | 0.86 | 0.91 | 0.91 | 0.89 | 0.00 | 0.82 | 0.80 | 0.83 | 0.90 |\n| classical monocyte | 440 | 0.85 | 0.88 | 0.88 | 0.85 | 0.00 | 0.81 | 0.81 | 0.84 | 0.90 |\n| plasma cell | 393 | 0.98 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| natural killer cell | 375 | 0.92 | 0.95 | 0.96 | 0.91 | 0.00 | 0.94 | 0.92 | 0.94 | 0.94 |\n| monocyte | 329 | 0.72 | 0.79 | 0.78 | 0.74 | 0.00 | 0.76 | 0.67 | 0.73 | 0.80 |\n| macrophage | 276 | 0.91 | 0.94 | 0.94 | 0.93 | 0.00 | 0.94 | 0.92 | 0.92 | 0.95 |\n| CD4-positive, alpha-beta T cell | 288 | 0.38 | 0.59 | 0.58 | 0.50 | 0.00 | 0.43 | 0.44 | 0.55 | 0.60 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 216 | 0.60 | 0.66 | 0.69 | 0.54 | 0.00 | 0.64 | 0.62 | 0.68 | 0.74 |\n| endothelial cell | 117 | 0.96 | 0.98 | 0.97 | 0.97 | 0.00 | 0.96 | 0.98 | 0.95 | 0.97 |\n| mature NK T cell | 104 | 0.67 | 0.72 | 0.78 | 0.43 | 0.00 | 0.69 | 0.60 | 0.68 | 0.75 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 61 | 0.50 | 0.31 | 0.64 | 0.23 | 0.00 | 0.55 | 0.44 | 0.49 | 0.57 |\n| erythrocyte | 48 | 0.90 | 0.98 | 0.97 | 0.99 | 0.00 | 0.95 | 0.98 | 0.84 | 0.98 |\n| intermediate monocyte | 33 | 0.15 | 0.06 | 0.30 | 0.05 | 0.00 | 0.22 | 0.29 | 0.32 | 0.32 |\n| regulatory T cell | 32 | 0.49 | 0.55 | 0.50 | 0.21 | 0.00 | 0.37 | 0.40 | 0.49 | 0.54 |\n| innate lymphoid cell | 24 | 0.81 | 0.90 | 0.94 | 0.82 | 0.00 | 0.80 | 0.82 | 0.89 | 0.91 |\n| T cell | 13 | 0.67 | 0.64 | 0.76 | 0.42 | 0.00 | 0.22 | 0.56 | 0.52 | 0.69 |\n| non-classical monocyte | 13 | 0.00 | 0.00 | 0.25 | 0.13 | 0.00 | 0.42 | 0.39 | 0.56 | 0.38 |\n| hematopoietic precursor cell | 9 | 0.62 | 0.62 | 0.80 | 0.75 | 0.00 | 0.80 | 0.70 | 0.78 | 0.84 |\n| platelet | 5 | 0.00 | 0.75 | 0.89 | 0.73 | 0.00 | 0.37 | 0.91 | 1.00 | 1.00 |\n| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.00 | 0.80 | 0.67 | 0.50 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| hematopoietic stem cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
+    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 14876 | 0.99 | 0.99 | 1.00 | 1.00 | 0.00 | 0.98 | 0.99 | 0.99 | 1.00 |\n| neutrophil | 13386 | 0.99 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta T cell | 9817 | 0.86 | 0.92 | 0.95 | 0.93 | 0.00 | 0.84 | 0.82 | 0.86 | 0.92 |\n| classical monocyte | 4022 | 0.83 | 0.85 | 0.90 | 0.88 | 0.00 | 0.82 | 0.82 | 0.85 | 0.90 |\n| plasma cell | 3583 | 0.98 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 3569 | 0.92 | 0.94 | 0.97 | 0.94 | 0.00 | 0.95 | 0.94 | 0.95 | 0.96 |\n| monocyte | 2785 | 0.66 | 0.73 | 0.83 | 0.79 | 0.00 | 0.76 | 0.70 | 0.77 | 0.83 |\n| macrophage | 2530 | 0.92 | 0.94 | 0.96 | 0.95 | 0.00 | 0.94 | 0.93 | 0.94 | 0.96 |\n| CD4-positive, alpha-beta T cell | 2454 | 0.38 | 0.55 | 0.70 | 0.64 | 0.00 | 0.51 | 0.53 | 0.63 | 0.69 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 2101 | 0.64 | 0.60 | 0.80 | 0.73 | 0.00 | 0.74 | 0.70 | 0.76 | 0.81 |\n| endothelial cell | 1233 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |\n| mature NK T cell | 925 | 0.68 | 0.78 | 0.86 | 0.63 | 0.00 | 0.74 | 0.67 | 0.73 | 0.84 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 561 | 0.47 | 0.14 | 0.76 | 0.47 | 0.00 | 0.58 | 0.52 | 0.55 | 0.66 |\n| erythrocyte | 358 | 0.90 | 0.98 | 0.98 | 0.98 | 0.00 | 0.93 | 0.98 | 0.86 | 0.98 |\n| intermediate monocyte | 363 | 0.14 | 0.03 | 0.34 | 0.28 | 0.00 | 0.41 | 0.47 | 0.50 | 0.63 |\n| regulatory T cell | 310 | 0.47 | 0.46 | 0.64 | 0.41 | 0.00 | 0.48 | 0.59 | 0.67 | 0.72 |\n| innate lymphoid cell | 146 | 0.68 | 0.80 | 0.91 | 0.80 | 0.00 | 0.71 | 0.82 | 0.86 | 0.86 |\n| T cell | 138 | 0.66 | 0.62 | 0.78 | 0.74 | 0.00 | 0.29 | 0.74 | 0.60 | 0.73 |\n| non-classical monocyte | 113 | 0.00 | 0.02 | 0.48 | 0.15 | 0.00 | 0.54 | 0.68 | 0.71 | 0.70 |\n| hematopoietic precursor cell | 59 | 0.54 | 0.72 | 0.84 | 0.81 | 0.00 | 0.79 | 0.77 | 0.83 | 0.85 |\n| platelet | 49 | 0.00 | 0.62 | 0.67 | 0.85 | 0.00 | 0.39 | 0.86 | 0.86 | 0.94 |\n| myeloid dendritic cell | 15 | 0.00 | 0.00 | 0.62 | 0.20 | 0.00 | 0.16 | 0.75 | 0.77 | 0.97 |\n| plasmacytoid dendritic cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 1.00 | 0.92 | 1.00 |\n| basophil | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 1.00 | 1.00 | 1.00 |\n| hematopoietic stem cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 1.00 | 1.00 | 0.00 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSG00000002587",
         "ENSG00000002919",
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+        "ENSG00000003249",
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         "ENSG00000013561",
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         "ENSG00000041353",
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         "ENSG00000064102",
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         "ENSG00000088899",
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         "ENSG00000120875",
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         "ENSG00000134247",
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